X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcommands%2FEditCommand.java;h=aff8595b99cb90981ff9730c7fbb089892e85145;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=ccc6a813692e1f32113b6ed01af246b1b591b758;hpb=04c49245650f804b89b88b6818fd8add2ef9343e;p=jalview.git

diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index ccc6a81..aff8595 100644
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -1,306 +1,483 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
  * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
  * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.commands;
 
-import java.util.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
 
-import jalview.datamodel.*;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.ListIterator;
 
 /**
- *
- * <p>Title: EditCommmand</p>
- *
- * <p>Description: Essential information for performing
- * undo and redo for cut/paste insert/delete gap
- * which can be stored in the HistoryList </p>
- *
- * <p>Copyright: Copyright (c) 2006</p>
- *
- * <p>Company: Dundee University</p>
- *
+ * 
+ * <p>
+ * Title: EditCommmand
+ * </p>
+ * 
+ * <p>
+ * Description: Essential information for performing undo and redo for cut/paste
+ * insert/delete gap which can be stored in the HistoryList
+ * </p>
+ * 
+ * <p>
+ * Copyright: Copyright (c) 2006
+ * </p>
+ * 
+ * <p>
+ * Company: Dundee University
+ * </p>
+ * 
  * @author not attributable
  * @version 1.0
  */
-public class EditCommand
-    implements CommandI
+public class EditCommand implements CommandI
 {
-  public static final int INSERT_GAP = 0;
-  public static final int DELETE_GAP = 1;
-  public static final int CUT = 2;
-  public static final int PASTE = 3;
-  public static final int REPLACE = 4;
+  public enum Action
+  {
+    INSERT_GAP, DELETE_GAP, CUT, PASTE, REPLACE, INSERT_NUC
+  };
 
-  Edit[] edits;
+  private List<Edit> edits = new ArrayList<Edit>();
 
   String description;
 
   public EditCommand()
-  {}
+  {
+  }
 
   public EditCommand(String description)
   {
     this.description = description;
   }
 
-  public EditCommand(String description,
-                     int command,
-                     SequenceI[] seqs,
-                     int position,
-                     int number,
-                     AlignmentI al)
+  public EditCommand(String description, Action command, SequenceI[] seqs,
+          int position, int number, AlignmentI al)
   {
     this.description = description;
-    if (command == CUT || command == PASTE)
+    if (command == Action.CUT || command == Action.PASTE)
     {
-      edits = new Edit[]
-          {
-          new Edit(command, seqs, position, number, al)};
+      setEdit(new Edit(command, seqs, position, number, al));
     }
 
-    performEdit(0);
+    performEdit(0, null);
   }
 
-  public EditCommand(String description,
-                     int command,
-                     String replace,
-                     SequenceI[] seqs,
-                     int position,
-                     int number,
-                     AlignmentI al)
+  public EditCommand(String description, Action command, String replace,
+          SequenceI[] seqs, int position, int number, AlignmentI al)
   {
     this.description = description;
-    if (command == REPLACE)
+    if (command == Action.REPLACE)
     {
-      edits = new Edit[]
-          { new Edit(command, seqs, position, number, al, replace)};
+      setEdit(new Edit(command, seqs, position, number, al, replace));
     }
 
-    performEdit(0);
+    performEdit(0, null);
+  }
+
+  /**
+   * Set the list of edits to the specified item (only).
+   * 
+   * @param e
+   */
+  protected void setEdit(Edit e)
+  {
+    edits.clear();
+    edits.add(e);
+  }
+
+  /**
+   * Add the given edit command to the stored list of commands.
+   * 
+   * @param e
+   */
+  protected void addEdit(Edit e)
+  {
+    edits.add(e);
+  }
+
+  /**
+   * Clear the list of stored edit commands.
+   * 
+   */
+  protected void clearEdits()
+  {
+    edits.clear();
+  }
+
+  /**
+   * Returns the i'th stored Edit command.
+   * 
+   * @param i
+   * @return
+   */
+  protected Edit getEdit(int i)
+  {
+    if (i >= 0 && i < edits.size())
+    {
+      return edits.get(i);
+    }
+    return null;
   }
 
+  @Override
   final public String getDescription()
   {
     return description;
   }
 
+  @Override
   public int getSize()
   {
-    return edits == null ? 0 : edits.length;
+    return edits.size();
   }
 
+  /**
+   * Return the alignment for the first edit (or null if no edit).
+   * 
+   * @return
+   */
   final public AlignmentI getAlignment()
   {
-    return edits[0].al;
+    return (edits.isEmpty() ? null : edits.get(0).al);
+  }
+
+  /**
+   * append a new editCommand Note. this shouldn't be called if the edit is an
+   * operation affects more alignment objects than the one referenced in al (for
+   * example, cut or pasting whole sequences). Use the form with an additional
+   * AlignmentI[] views parameter.
+   * 
+   * @param command
+   * @param seqs
+   * @param position
+   * @param number
+   * @param al
+   * @param performEdit
+   */
+  final public void appendEdit(Action command, SequenceI[] seqs,
+          int position,
+          int number, AlignmentI al, boolean performEdit)
+  {
+    appendEdit(command, seqs, position, number, al, performEdit, null);
   }
 
-  final public void appendEdit(int command,
-                               SequenceI[] seqs,
-                               int position,
-                               int number,
-                               AlignmentI al,
-                               boolean performEdit)
+  /**
+   * append a new edit command with a set of alignment views that may be
+   * operated on
+   * 
+   * @param command
+   * @param seqs
+   * @param position
+   * @param number
+   * @param al
+   * @param performEdit
+   * @param views
+   */
+  final public void appendEdit(Action command, SequenceI[] seqs,
+          int position,
+          int number, AlignmentI al, boolean performEdit, AlignmentI[] views)
   {
-    Edit edit = new Edit(command, seqs, position, number, al.getGapCharacter());
+    Edit edit = new Edit(command, seqs, position, number,
+            al.getGapCharacter());
     if (al.getHeight() == seqs.length)
     {
       edit.al = al;
       edit.fullAlignmentHeight = true;
     }
 
-    if (edits != null)
-    {
-      Edit[] temp = new Edit[edits.length + 1];
-      System.arraycopy(edits, 0, temp, 0, edits.length);
-      edits = temp;
-      edits[edits.length - 1] = edit;
-    }
-    else
-    {
-      edits = new Edit[]
-          {
-          edit};
-    }
+    edits.add(edit);
 
     if (performEdit)
     {
-      performEdit(edits.length - 1);
+      performEdit(edit, views);
     }
   }
 
-  final void performEdit(int commandIndex)
+  /**
+   * Execute all the edit commands, starting at the given commandIndex
+   * 
+   * @param commandIndex
+   * @param views
+   */
+  final void performEdit(int commandIndex, AlignmentI[] views)
   {
-    int eSize = edits.length;
-    for (int e = commandIndex; e < eSize; e++)
+    ListIterator<Edit> iterator = edits.listIterator(commandIndex);
+    while (iterator.hasNext())
     {
-      switch(edits[e].command)
-      {
-        case INSERT_GAP:
-          insertGap(edits[e]);
-          break;
-        case DELETE_GAP:
-          deleteGap(edits[e]);
-          break;
-        case CUT:
-          cut(edits[e]);
-          break;
-        case PASTE:
-          paste(edits[e]);
-          break;
-        case REPLACE:
-          replace(edits[e]);
-          break;
-      }
+      Edit edit = iterator.next();
+      performEdit(edit, views);
     }
   }
 
-  final public void doCommand()
+  /**
+   * Execute one edit command in all the specified alignment views
+   * 
+   * @param edit
+   * @param views
+   */
+  protected void performEdit(Edit edit, AlignmentI[] views)
   {
-    performEdit(0);
+    switch (edit.command)
+    {
+    case INSERT_GAP:
+      insertGap(edit);
+      break;
+    case DELETE_GAP:
+      deleteGap(edit);
+      break;
+    case CUT:
+      cut(edit, views);
+      break;
+    case PASTE:
+      paste(edit, views);
+      break;
+    case REPLACE:
+      replace(edit);
+      break;
+    case INSERT_NUC:
+      // TODO:add deleteNuc for UNDO
+      // case INSERT_NUC:
+      // insertNuc(edits[e]);
+      break;
+    default:
+      break;
+    }
   }
 
-  final public void undoCommand()
+  @Override
+  final public void doCommand(AlignmentI[] views)
   {
-    int e = 0, eSize = edits.length;
-    for (e = eSize - 1; e > -1; e--)
+    performEdit(0, views);
+  }
+
+  /**
+   * Undo the stored list of commands, in reverse order.
+   */
+  @Override
+  final public void undoCommand(AlignmentI[] views)
+  { 
+    ListIterator<Edit> iterator = edits.listIterator(edits.size());
+    while (iterator.hasPrevious())
     {
-      switch (edits[e].command)
+      Edit e = iterator.previous();
+      switch (e.command)
       {
-        case INSERT_GAP:
-          deleteGap(edits[e]);
-          break;
-        case DELETE_GAP:
-          insertGap(edits[e]);
-          break;
-        case CUT:
-          paste(edits[e]);
-          break;
-        case PASTE:
-          cut(edits[e]);
-          break;
-        case REPLACE:
-          replace(edits[e]);
-          break;
+      case INSERT_GAP:
+        deleteGap(e);
+        break;
+      case DELETE_GAP:
+        insertGap(e);
+        break;
+      case CUT:
+        paste(e, views);
+        break;
+      case PASTE:
+        cut(e, views);
+        break;
+      case REPLACE:
+        replace(e);
+        break;
+      case INSERT_NUC:
+        // not implemented
+        break;
+      default:
+        break;
       }
     }
   }
 
-  final void insertGap(Edit command)
+  /**
+   * Insert gap(s) in sequences as specified by the command, and adjust
+   * annotations.
+   * 
+   * @param command
+   */
+  final private void insertGap(Edit command)
   {
+
     for (int s = 0; s < command.seqs.length; s++)
     {
-      command.seqs[s].insertCharAt(command.position,
-                                   command.number,
-                                   command.gapChar);
+      command.seqs[s].insertCharAt(command.position, command.number,
+              command.gapChar);
+      // System.out.println("pos: "+command.position+" number: "+command.number);
     }
 
-    adjustAnnotations(command, true, false);
+    adjustAnnotations(command, true, false, null);
   }
 
-  final void deleteGap(Edit command)
+  //
+  // final void insertNuc(Edit command)
+  // {
+  //
+  // for (int s = 0; s < command.seqs.length; s++)
+  // {
+  // System.out.println("pos: "+command.position+" number: "+command.number);
+  // command.seqs[s].insertCharAt(command.position, command.number,'A');
+  // }
+  //
+  // adjustAnnotations(command, true, false, null);
+  // }
+
+  /**
+   * Delete gap(s) in sequences as specified by the command, and adjust
+   * annotations.
+   * 
+   * @param command
+   */
+  final private void deleteGap(Edit command)
   {
     for (int s = 0; s < command.seqs.length; s++)
     {
-      command.seqs[s].deleteChars(command.position,
-                                  command.position + command.number);
+      command.seqs[s].deleteChars(command.position, command.position
+              + command.number);
     }
 
-    adjustAnnotations(command, false, false);
+    adjustAnnotations(command, false, false, null);
   }
 
-  void cut(Edit command)
+  /**
+   * Carry out a Cut action. The cut characters are saved in case Undo is
+   * requested.
+   * 
+   * @param command
+   * @param views
+   */
+  void cut(Edit command, AlignmentI[] views)
   {
-    boolean seqDeleted=false;
+    boolean seqDeleted = false;
     command.string = new char[command.seqs.length][];
 
     for (int i = 0; i < command.seqs.length; i++)
     {
-      if (command.seqs[i].getLength() > command.position)
+      final SequenceI sequence = command.seqs[i];
+      if (sequence.getLength() > command.position)
       {
-        command.string[i] = command.seqs[i].getSequence(command.position,
-            command.position + command.number);
-
-        if (command.seqs[i].getDatasetSequence() != null
-            || command.seqs[i].getSequenceFeatures() != null)
+        command.string[i] = sequence.getSequence(command.position,
+                command.position + command.number);
+        SequenceI oldds = sequence.getDatasetSequence();
+        if (command.oldds != null && command.oldds[i] != null)
         {
-          for (int s = command.position; s < command.position + command.number;
-               s++)
+          // we are redoing an undone cut.
+          sequence.setDatasetSequence(null);
+        }
+        sequence.deleteChars(command.position, command.position
+                + command.number);
+        if (command.oldds != null && command.oldds[i] != null)
+        {
+          // oldds entry contains the cut dataset sequence.
+          sequence.setDatasetSequence(command.oldds[i]);
+          command.oldds[i] = oldds;
+        }
+        else
+        {
+          // modify the oldds if necessary
+          if (oldds != sequence.getDatasetSequence()
+                  || sequence.getSequenceFeatures() != null)
           {
-            if (jalview.schemes.ResidueProperties
-                .aaIndex[command.seqs[i].getCharAt(s)] != 23)
+            if (command.oldds == null)
             {
-              adjustFeatures(command, i,
-                             command.seqs[i].findPosition(command.position),
-                             command.seqs[i].findPosition(command.position +
-                  command.number),
-                             false);
-              break;
+              command.oldds = new SequenceI[command.seqs.length];
             }
+            command.oldds[i] = oldds;
+            adjustFeatures(
+                    command,
+                    i,
+                    sequence.findPosition(command.position),
+                    sequence.findPosition(command.position
+                            + command.number), false);
           }
         }
-        command.seqs[i].deleteChars(command.position,
-                                    command.position + command.number);
       }
 
-      if (command.seqs[i].getLength() < 1)
+      if (sequence.getLength() < 1)
       {
-        command.al.deleteSequence(command.seqs[i]);
-        seqDeleted=true;
+        command.al.deleteSequence(sequence);
+        seqDeleted = true;
       }
     }
 
-    adjustAnnotations(command, false, seqDeleted);
+    adjustAnnotations(command, false, seqDeleted, views);
   }
 
-  void paste(Edit command)
+  /**
+   * Perform the given Paste command. This may be to add cut or copied sequences
+   * to an alignment, or to undo a 'Cut' action on a region of the alignment.
+   * 
+   * @param command
+   * @param views
+   */
+  void paste(Edit command, AlignmentI[] views)
   {
     StringBuffer tmp;
     boolean newDSNeeded;
-    boolean seqWasDeleted=false;
+    boolean newDSWasNeeded;
+    int newstart, newend;
+    boolean seqWasDeleted = false;
     int start = 0, end = 0;
 
     for (int i = 0; i < command.seqs.length; i++)
     {
       newDSNeeded = false;
+      newDSWasNeeded = command.oldds != null && command.oldds[i] != null;
       if (command.seqs[i].getLength() < 1)
       {
         // ie this sequence was deleted, we need to
         // read it to the alignment
         if (command.alIndex[i] < command.al.getHeight())
         {
-          command.al.getSequences().insertElementAt(command.seqs[i],
-              command.alIndex[i]);
+          List<SequenceI> sequences;
+          synchronized (sequences = command.al.getSequences())
+          {
+            if (!(command.alIndex[i] < 0))
+            {
+              sequences.add(command.alIndex[i], command.seqs[i]);
+            }
+          }
         }
         else
         {
           command.al.addSequence(command.seqs[i]);
         }
-        seqWasDeleted=true;
+        seqWasDeleted = true;
       }
+      newstart = command.seqs[i].getStart();
+      newend = command.seqs[i].getEnd();
+
       tmp = new StringBuffer();
       tmp.append(command.seqs[i].getSequence());
+      // Undo of a delete does not replace original dataset sequence on to
+      // alignment sequence.
 
       if (command.string != null && command.string[i] != null)
       {
         if (command.position >= tmp.length())
         {
-          //This occurs if padding is on, and residues
-          //are removed from end of alignment
+          // This occurs if padding is on, and residues
+          // are removed from end of alignment
           int length = command.position - tmp.length();
           while (length > 0)
           {
@@ -309,43 +486,64 @@ public class EditCommand
           }
         }
         tmp.insert(command.position, command.string[i]);
-
         for (int s = 0; s < command.string[i].length; s++)
         {
-          if (jalview.schemes.ResidueProperties.aaIndex[command.string[i][s]] !=
-              23)
+          if (jalview.schemes.ResidueProperties.aaIndex[command.string[i][s]] != 23)
           {
-            newDSNeeded = true;
-            start = command.seqs[i].findPosition(command.position);
-            end = command.seqs[i].findPosition(command.position +
-                                               command.number);
-            break;
+            if (!newDSNeeded)
+            {
+              newDSNeeded = true;
+              start = command.seqs[i].findPosition(command.position);
+              end = command.seqs[i].findPosition(command.position
+                      + command.number);
+            }
+            if (command.seqs[i].getStart() == start)
+            {
+              newstart--;
+            }
+            else
+            {
+              newend++;
+            }
           }
         }
         command.string[i] = null;
       }
 
       command.seqs[i].setSequence(tmp.toString());
-
+      command.seqs[i].setStart(newstart);
+      command.seqs[i].setEnd(newend);
       if (newDSNeeded)
       {
         if (command.seqs[i].getDatasetSequence() != null)
-        { // use new ds mechanism here
-          Sequence ds = new Sequence(command.seqs[i].getName(),
-                                     jalview.analysis.AlignSeq.extractGaps(
-                                         jalview.util.Comparison.GapChars,
-                                         command.seqs[i].getSequenceAsString()
-                                     ),
-                                     command.seqs[i].getStart(),
-                                     command.seqs[i].getEnd());
-          ds.setDescription(command.seqs[i].getDescription());
+        {
+          SequenceI ds;
+          if (newDSWasNeeded)
+          {
+            ds = command.oldds[i];
+          }
+          else
+          {
+            // make a new DS sequence
+            // use new ds mechanism here
+            ds = new Sequence(command.seqs[i].getName(),
+                    jalview.analysis.AlignSeq.extractGaps(
+                            jalview.util.Comparison.GapChars,
+                            command.seqs[i].getSequenceAsString()),
+                    command.seqs[i].getStart(), command.seqs[i].getEnd());
+            ds.setDescription(command.seqs[i].getDescription());
+          }
+          if (command.oldds == null)
+          {
+            command.oldds = new SequenceI[command.seqs.length];
+          }
+          command.oldds[i] = command.seqs[i].getDatasetSequence();
           command.seqs[i].setDatasetSequence(ds);
         }
-
         adjustFeatures(command, i, start, end, true);
       }
     }
-    adjustAnnotations(command, true, seqWasDeleted);
+    adjustAnnotations(command, true, seqWasDeleted, views);
 
     command.string = null;
   }
@@ -356,29 +554,86 @@ public class EditCommand
     String oldstring;
     int start = command.position;
     int end = command.number;
-
+    // TODO TUTORIAL - Fix for replacement with different length of sequence (or
+    // whole sequence)
+    // TODO Jalview 2.4 bugfix change to an aggregate command - original
+    // sequence string is cut, new string is pasted in.
     command.number = start + command.string[0].length;
     for (int i = 0; i < command.seqs.length; i++)
     {
+      boolean newDSWasNeeded = command.oldds != null
+              && command.oldds[i] != null;
+
+      /**
+       * cut addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT,
+       * cut, sg.getStartRes(), sg.getEndRes()-sg.getStartRes()+1,
+       * viewport.alignment));
+       * 
+       */
+      /**
+       * then addHistoryItem(new EditCommand( "Add sequences",
+       * EditCommand.PASTE, sequences, 0, alignment.getWidth(), alignment) );
+       * 
+       */
       oldstring = command.seqs[i].getSequenceAsString();
       tmp = new StringBuffer(oldstring.substring(0, start));
       tmp.append(command.string[i]);
+      String nogaprep = jalview.analysis.AlignSeq.extractGaps(
+              jalview.util.Comparison.GapChars, new String(
+                      command.string[i]));
+      int ipos = command.seqs[i].findPosition(start)
+              - command.seqs[i].getStart();
       tmp.append(oldstring.substring(end));
       command.seqs[i].setSequence(tmp.toString());
       command.string[i] = oldstring.substring(start, end).toCharArray();
+      String nogapold = jalview.analysis.AlignSeq.extractGaps(
+              jalview.util.Comparison.GapChars, new String(
+                      command.string[i]));
+      if (!nogaprep.toLowerCase().equals(nogapold.toLowerCase()))
+      {
+        if (newDSWasNeeded)
+        {
+          SequenceI oldds = command.seqs[i].getDatasetSequence();
+          command.seqs[i].setDatasetSequence(command.oldds[i]);
+          command.oldds[i] = oldds;
+        }
+        else
+        {
+          if (command.oldds == null)
+          {
+            command.oldds = new SequenceI[command.seqs.length];
+          }
+          command.oldds[i] = command.seqs[i].getDatasetSequence();
+          SequenceI newds = new Sequence(
+                  command.seqs[i].getDatasetSequence());
+          String fullseq, osp = newds.getSequenceAsString();
+          fullseq = osp.substring(0, ipos) + nogaprep
+                  + osp.substring(ipos + nogaprep.length());
+          newds.setSequence(fullseq.toUpperCase());
+          // TODO: JAL-1131 ensure newly created dataset sequence is added to
+          // the set of
+          // dataset sequences associated with the alignment.
+          // TODO: JAL-1131 fix up any annotation associated with new dataset
+          // sequence to ensure that original sequence/annotation relationships
+          // are preserved.
+          command.seqs[i].setDatasetSequence(newds);
+
+        }
+      }
       tmp = null;
       oldstring = null;
     }
   }
 
-  final void adjustAnnotations(Edit command, boolean insert, boolean modifyVisibility)
+  final void adjustAnnotations(Edit command, boolean insert,
+          boolean modifyVisibility, AlignmentI[] views)
   {
     AlignmentAnnotation[] annotations = null;
 
     if (modifyVisibility && !insert)
     {
       // only occurs if a sequence was added or deleted.
-      command.deletedAnnotationRows = new Hashtable();
+      command.deletedAnnotationRows = new Hashtable<SequenceI, AlignmentAnnotation[]>();
     }
     if (command.fullAlignmentHeight)
     {
@@ -393,32 +648,108 @@ public class EditCommand
         if (modifyVisibility)
         {
           // Rows are only removed or added to sequence object.
-          if (!insert) {
+          if (!insert)
+          {
             // remove rows
             tmp = command.seqs[s].getAnnotation();
-            if (tmp!=null) {
-              command.deletedAnnotationRows.put(command.seqs[s], tmp);
-              for (int aa =0; aa<tmp.length; aa++)
+            if (tmp != null)
+            {
+              int alen = tmp.length;
+              for (int aa = 0; aa < tmp.length; aa++)
               {
-                command.al.deleteAnnotation(tmp[aa]);
+                if (!command.al.deleteAnnotation(tmp[aa]))
+                {
+                  // strip out annotation not in the current al (will be put
+                  // back on insert in all views)
+                  tmp[aa] = null;
+                  alen--;
+                }
               }
               command.seqs[s].setAlignmentAnnotation(null);
+              if (alen != tmp.length)
+              {
+                // save the non-null annotation references only
+                AlignmentAnnotation[] saved = new AlignmentAnnotation[alen];
+                for (int aa = 0, aapos = 0; aa < tmp.length; aa++)
+                {
+                  if (tmp[aa] != null)
+                  {
+                    saved[aapos++] = tmp[aa];
+                    tmp[aa] = null;
+                  }
+                }
+                tmp = saved;
+                command.deletedAnnotationRows.put(command.seqs[s], saved);
+                // and then remove any annotation in the other views
+                for (int alview = 0; views != null && alview < views.length; alview++)
+                {
+                  if (views[alview] != command.al)
+                  {
+                    AlignmentAnnotation[] toremove = views[alview]
+                            .getAlignmentAnnotation();
+                    if (toremove == null || toremove.length == 0)
+                    {
+                      continue;
+                    }
+                    // remove any alignment annotation on this sequence that's
+                    // on that alignment view.
+                    for (int aa = 0; aa < toremove.length; aa++)
+                    {
+                      if (toremove[aa].sequenceRef == command.seqs[s])
+                      {
+                        views[alview].deleteAnnotation(toremove[aa]);
+                      }
+                    }
+                  }
+                }
+              }
+              else
+              {
+                // save all the annotation
+                command.deletedAnnotationRows.put(command.seqs[s], tmp);
+              }
             }
-          } else {
+          }
+          else
+          {
             // recover rows
-            if (command.deletedAnnotationRows!=null && command.deletedAnnotationRows.containsKey(command.seqs[s]))
+            if (command.deletedAnnotationRows != null
+                    && command.deletedAnnotationRows
+                            .containsKey(command.seqs[s]))
             {
-              AlignmentAnnotation[] revealed = (AlignmentAnnotation[]) command.deletedAnnotationRows.get(command.seqs[s]);
+              AlignmentAnnotation[] revealed = command.deletedAnnotationRows
+                      .get(command.seqs[s]);
               command.seqs[s].setAlignmentAnnotation(revealed);
-              if (revealed!=null) {
-                for (int aa =0; aa<revealed.length; aa++)
+              if (revealed != null)
+              {
+                for (int aa = 0; aa < revealed.length; aa++)
                 {
+                  // iterate through al adding original annotation
                   command.al.addAnnotation(revealed[aa]);
                 }
-                for (int aa =0; aa<revealed.length; aa++)
+                for (int aa = 0; aa < revealed.length; aa++)
                 {
                   command.al.setAnnotationIndex(revealed[aa], aa);
                 }
+                // and then duplicate added annotation on every other alignment
+                // view
+                for (int vnum = 0; views != null && vnum < views.length; vnum++)
+                {
+                  if (views[vnum] != command.al)
+                  {
+                    int avwidth = views[vnum].getWidth() + 1;
+                    // duplicate in this view
+                    for (int a = 0; a < revealed.length; a++)
+                    {
+                      AlignmentAnnotation newann = new AlignmentAnnotation(
+                              revealed[a]);
+                      command.seqs[s].addAlignmentAnnotation(newann);
+                      newann.padAnnotation(avwidth);
+                      views[vnum].addAnnotation(newann);
+                      views[vnum].setAnnotationIndex(newann, a);
+                    }
+                  }
+                }
               }
             }
           }
@@ -436,14 +767,13 @@ public class EditCommand
         }
         else
         {
-          tmp = new AlignmentAnnotation
-              [aSize + command.seqs[s].getAnnotation().length];
+          tmp = new AlignmentAnnotation[aSize
+                  + command.seqs[s].getAnnotation().length];
 
           System.arraycopy(annotations, 0, tmp, 0, aSize);
 
-          System.arraycopy(command.seqs[s].getAnnotation(),
-                           0, tmp, aSize,
-                           command.seqs[s].getAnnotation().length);
+          System.arraycopy(command.seqs[s].getAnnotation(), 0, tmp, aSize,
+                  command.seqs[s].getAnnotation().length);
 
           annotations = tmp;
         }
@@ -458,14 +788,15 @@ public class EditCommand
 
     if (!insert)
     {
-      command.deletedAnnotations = new Hashtable();
+      command.deletedAnnotations = new Hashtable<String, Annotation[]>();
     }
 
     int aSize;
     Annotation[] temp;
     for (int a = 0; a < annotations.length; a++)
     {
-      if (annotations[a].autoCalculated)
+      if (annotations[a].autoCalculated
+              || annotations[a].annotations == null)
       {
         continue;
       }
@@ -476,25 +807,25 @@ public class EditCommand
       if (insert)
       {
         temp = new Annotation[aSize + command.number];
-        if(annotations[a].padGaps)
+        if (annotations[a].padGaps)
+        {
           for (int aa = 0; aa < temp.length; aa++)
           {
-            temp[aa] = new Annotation(
-                command.al.getGapCharacter()+"",
-                null, ' ', 0);
+            temp[aa] = new Annotation(command.gapChar + "", null, ' ', 0);
           }
+        }
       }
       else
       {
         if (command.position < aSize)
         {
-          if (command.position + command.number > aSize)
+          if (command.position + command.number >= aSize)
           {
             tSize = aSize;
           }
           else
           {
-            tSize = aSize - command.number + command.position;
+            tSize = aSize - command.number;
           }
         }
         else
@@ -507,54 +838,46 @@ public class EditCommand
           tSize = aSize;
         }
         temp = new Annotation[tSize];
-
       }
 
       if (insert)
       {
         if (command.position < annotations[a].annotations.length)
         {
-          System.arraycopy(annotations[a].annotations,
-                           0, temp, 0, command.position);
+          System.arraycopy(annotations[a].annotations, 0, temp, 0,
+                  command.position);
 
           if (command.deletedAnnotations != null
-              &&
-              command.deletedAnnotations.containsKey(annotations[a].
-              annotationId))
+                  && command.deletedAnnotations
+                          .containsKey(annotations[a].annotationId))
           {
-            Annotation[] restore = (Annotation[])
-                command.deletedAnnotations.get(annotations[a].annotationId);
+            Annotation[] restore = command.deletedAnnotations
+                    .get(annotations[a].annotationId);
 
-            System.arraycopy(restore,
-                             0,
-                             temp,
-                             command.position,
-                             command.number);
+            System.arraycopy(restore, 0, temp, command.position,
+                    command.number);
 
           }
 
-          System.arraycopy(annotations[a].annotations,
-                           command.position, temp,
-                           command.position + command.number,
-                           aSize - command.position);
+          System.arraycopy(annotations[a].annotations, command.position,
+                  temp, command.position + command.number, aSize
+                          - command.position);
         }
         else
         {
           if (command.deletedAnnotations != null
-              &&
-              command.deletedAnnotations.containsKey(annotations[a].
-              annotationId))
+                  && command.deletedAnnotations
+                          .containsKey(annotations[a].annotationId))
           {
-            Annotation[] restore = (Annotation[])
-                command.deletedAnnotations.get(annotations[a].annotationId);
-
-            temp = new Annotation[annotations[a].annotations.length +
-                restore.length];
-            System.arraycopy(annotations[a].annotations,
-                             0, temp, 0,
-                             annotations[a].annotations.length);
+            Annotation[] restore = command.deletedAnnotations
+                    .get(annotations[a].annotationId);
+
+            temp = new Annotation[annotations[a].annotations.length
+                    + restore.length];
+            System.arraycopy(annotations[a].annotations, 0, temp, 0,
+                    annotations[a].annotations.length);
             System.arraycopy(restore, 0, temp,
-                             annotations[a].annotations.length, restore.length);
+                    annotations[a].annotations.length, restore.length);
           }
           else
           {
@@ -566,15 +889,20 @@ public class EditCommand
       {
         if (tSize != aSize || command.position < 2)
         {
-          int copylen = Math.min(command.position, annotations[a].annotations.length);
-          if (copylen>0)
-            System.arraycopy(annotations[a].annotations,
-                           0, temp, 0, copylen); //command.position);
+          int copylen = Math.min(command.position,
+                  annotations[a].annotations.length);
+          if (copylen > 0)
+           {
+            System.arraycopy(annotations[a].annotations, 0, temp, 0,
+                    copylen); // command.position);
+          }
 
           Annotation[] deleted = new Annotation[command.number];
-          if (copylen>command.position) {
-            copylen = Math.min(command.number, annotations[a].annotations.length-command.position);
-            if (copylen>0)
+          if (copylen >= command.position)
+          {
+            copylen = Math.min(command.number,
+                    annotations[a].annotations.length - command.position);
+            if (copylen > 0)
             {
               System.arraycopy(annotations[a].annotations,
                       command.position, deleted, 0, copylen); // command.number);
@@ -582,12 +910,14 @@ public class EditCommand
           }
 
           command.deletedAnnotations.put(annotations[a].annotationId,
-                                         deleted);
-          if (annotations[a].annotations.length>command.position+command.number) {
-            System.arraycopy(annotations[a].annotations,
-                           command.position + command.number,
-                           temp, command.position,
-                           annotations[a].annotations.length - command.position - command.number); // aSize
+                  deleted);
+          if (annotations[a].annotations.length > command.position
+                  + command.number)
+          {
+            System.arraycopy(annotations[a].annotations, command.position
+                    + command.number, temp, command.position,
+                    annotations[a].annotations.length - command.position
+                            - command.number); // aSize
           }
         }
         else
@@ -597,17 +927,16 @@ public class EditCommand
           if (dSize > 0)
           {
             Annotation[] deleted = new Annotation[command.number];
-            System.arraycopy(annotations[a].annotations,
-                             command.position, deleted, 0, dSize);
+            System.arraycopy(annotations[a].annotations, command.position,
+                    deleted, 0, dSize);
 
             command.deletedAnnotations.put(annotations[a].annotationId,
-                                           deleted);
+                    deleted);
 
             tSize = Math.min(annotations[a].annotations.length,
-                             command.position);
+                    command.position);
             temp = new Annotation[tSize];
-            System.arraycopy(annotations[a].annotations,
-                             0, temp, 0, tSize);
+            System.arraycopy(annotations[a].annotations, 0, temp, 0, tSize);
           }
           else
           {
@@ -621,7 +950,7 @@ public class EditCommand
   }
 
   final void adjustFeatures(Edit command, int index, int i, int j,
-                            boolean insert)
+          boolean insert)
   {
     SequenceI seq = command.seqs[index];
     SequenceI sequence = seq.getDatasetSequence();
@@ -633,11 +962,10 @@ public class EditCommand
     if (insert)
     {
       if (command.editedFeatures != null
-          && command.editedFeatures.containsKey(seq))
+              && command.editedFeatures.containsKey(seq))
       {
-        sequence.setSequenceFeatures(
-            (SequenceFeature[]) command.editedFeatures.get(seq)
-            );
+        sequence.setSequenceFeatures(command.editedFeatures
+                .get(seq));
       }
 
       return;
@@ -692,7 +1020,7 @@ public class EditCommand
 
     if (command.editedFeatures == null)
     {
-      command.editedFeatures = new Hashtable();
+      command.editedFeatures = new Hashtable<SequenceI, SequenceFeature[]>();
     }
 
     command.editedFeatures.put(seq, oldsf);
@@ -701,23 +1029,32 @@ public class EditCommand
 
   class Edit
   {
+    public SequenceI[] oldds;
+
     boolean fullAlignmentHeight = false;
-    Hashtable deletedAnnotationRows;
-    Hashtable deletedAnnotations;
-    Hashtable editedFeatures;
+
+    Hashtable<SequenceI, AlignmentAnnotation[]> deletedAnnotationRows;
+
+    Hashtable<String, Annotation[]> deletedAnnotations;
+
+    Hashtable<SequenceI, SequenceFeature[]> editedFeatures;
+
     AlignmentI al;
-    int command;
+
+    Action command;
+
     char[][] string;
+
     SequenceI[] seqs;
+
     int[] alIndex;
+
     int position, number;
+
     char gapChar;
 
-    Edit(int command,
-         SequenceI[] seqs,
-         int position,
-         int number,
-         char gapChar)
+    Edit(Action command, SequenceI[] seqs, int position, int number,
+            char gapChar)
     {
       this.command = command;
       this.seqs = seqs;
@@ -726,11 +1063,8 @@ public class EditCommand
       this.gapChar = gapChar;
     }
 
-    Edit(int command,
-         SequenceI[] seqs,
-         int position,
-         int number,
-         AlignmentI al)
+    Edit(Action command, SequenceI[] seqs, int position, int number,
+            AlignmentI al)
     {
       this.gapChar = al.getGapCharacter();
       this.command = command;
@@ -748,18 +1082,15 @@ public class EditCommand
       fullAlignmentHeight = (al.getHeight() == seqs.length);
     }
 
-    Edit(int command,
-         SequenceI[] seqs,
-         int position,
-         int number,
-         AlignmentI al,
-         String replace)
+    Edit(Action command, SequenceI[] seqs, int position, int number,
+            AlignmentI al, String replace)
     {
       this.command = command;
       this.seqs = seqs;
       this.position = position;
       this.number = number;
       this.al = al;
+      this.gapChar = al.getGapCharacter();
       string = new char[seqs.length][];
       for (int i = 0; i < seqs.length; i++)
       {
@@ -769,5 +1100,4 @@ public class EditCommand
       fullAlignmentHeight = (al.getHeight() == seqs.length);
     }
   }
-
 }